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  • $\begingroup$ So MorphologicalGraph really is implemented in pure Mathematica ... I had no idea. I was so sure it must have been something lower level that I didn't even try to check the source. $\endgroup$ Commented Jun 15, 2018 at 16:15
  • $\begingroup$ The key function is Image`MorphologicalOperationsDump`ConstrainedMComponents, and internally it just uses a kernel function. I guess this is what does the shortest path calculation, but it is not 100% clear to me how to use it. $\endgroup$ Commented Jun 15, 2018 at 16:16